1. Field of the Invention
The disclosed embodiments relate to nucleic acid constructs and methods of using these constructs to rapidly detect target molecule interactions. The switches can have applications in sensing the presence of targets, including proteins, nucleic acids, organisms, environmental contaminants, bioterror agents, and/or pharmaceutical agents. The switches should facilitate processes to screen lead compounds for drug development that have high affinity for a target molecule and/or target complex. Embodiments of the invention to screen potential drugs effective against HIV-1 are used to illustrate the invention. The molecular switches are also applicable to processes in molecular electronics and nano-devices.
2. Description of the Related Art
HIV-disease causes great suffering and death in the U.S., and millions are dying worldwide. Even though the number of deaths in the United States from HIV-disease has declined in recent years, the worldwide epidemic is out of control. This ever-larger number of infected people is a direct threat to everyone because HIV-1 mutates so rapidly. The larger the pool of infected individuals, the more rapidly drug-resistant strains will emerge. The reverse transcriptase makes so many errors that every single point mutation occurs daily in newly infected cells (Coffin, J. M. (1995) Science 267:483-9), and nearly 1% of all possible double mutations occur (Perelson, A. S. et al. (1997) AIDS 11 (suppl. A) S17-34). Combinations of drugs used in “Highly Active AntiRetroviral Therapy” (HAART) treatment regimes target different parts of the viral life cycle. In the face of such a high mutation rate, it is clear that failures in the HAART approach must occur with increasing frequency using existing drugs. Resistant strains already exist for all currently used protease and reverse transcriptase inhibitors (Pillay, D. et al. (2000) Rev. Med. Viral. 10:231-53), the most potent weapons in the battle against AIDS.
Even if an effective vaccine is developed to prevent new HIV-1 infections, there will still remain a need to treat millions of AIDS victims. Their long-term treatment will require new generations of drugs. Anti-nucleocapsid protein drugs, as well as agents directed at other potential HIV targets, such as anti-rev and anti-tat, could be combined with current and next generation drugs for a multi-pronged attack that would be difficult for the virus to evade. Adding these drugs to present HAART treatments may provide highly specific and potent antiretroviral treatments. Such drugs may greatly diminish the devastating effects of HIV-related disease around the world.
Scores of other human and animal disease states have been related to interactions of biomolecules with other molecules. These biomolecules present targets for therapeutic intervention. This is a current focus for many academic and industrial efforts to generate new pharmaceuticals. The current invention can accelerate drug discovery. Examples include, but are not limited to, kinases and phosphatases involved in signaling cascades.
Detection of environmental contaminants and terrorist agents has become an important focus of public concern. The current invention can be applied to the detection of most agents that interest the Environmental Protection Agency (EPA) (http://www.epa.gov/safewater/mcl.html#mcls) and on the select agents list monitored by the Centers for Disease Control (CDC), the National Institute of Allergy and Infectious Diseases (NIAID) (http://www2.niaid.nih.gov/Biodefense/bandc_priority.htm), and the Homeland Security Agency (HSA). The current invention provides a technology for near real-time detection of environmental and terrorist agents. Examples include, but are not limited to, cryptosporidium and giardia, which contaminate public water supplies, and ricin, anthrax and ebola virus, which are agents for bio-terrorism and bio-warfare.
Molecules that can switch between stable states are of interest for nanoelectronics, nanofabrication, and nanomachines. The present invention is of special interest in high density information storage devices used in nanoelectronic applications. Read, write, and erase functions can be constructed using the subject invention. It is also contemplated that subject molecular switches could be coupled to build materials and machines on the molecular scale.